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<li class="navelem"><b>claragenomics</b></li><li class="navelem"><b>cudapoa</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a></li>  </ul>
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<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="classclaragenomics_1_1cudapoa_1_1Batch-members.html">List of all members</a>  </div>
  <div class="headertitle">
<div class="title">claragenomics::cudapoa::Batch Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span><div class="ingroups"><a class="el" href="group__cudapoa.html">CUDA POA package</a></div></div>  </div>
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<p><code>#include &lt;<a class="el" href="batch_8hpp_source.html">batch.hpp</a>&gt;</code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:ab70c94f0a2b161abd8fce03f487c2db1"><td class="memItemLeft" align="right" valign="top"><a id="ab70c94f0a2b161abd8fce03f487c2db1"></a>
virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">~Batch</a> ()=default</td></tr>
<tr class="memdesc:ab70c94f0a2b161abd8fce03f487c2db1"><td class="mdescLeft">&#160;</td><td class="mdescRight">CudapoaBatch has a custom dtor, so declare ~Batch virtual and give it a default implementation. <br /></td></tr>
<tr class="separator:ab70c94f0a2b161abd8fce03f487c2db1"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a8f2f44e7b4d7f51d8ba68323841dcdf0"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a8f2f44e7b4d7f51d8ba68323841dcdf0">add_poa_group</a> (std::vector&lt; <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> &gt; &amp;per_seq_status, const <a class="el" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">Group</a> &amp;poa_group)=0</td></tr>
<tr class="memdesc:a8f2f44e7b4d7f51d8ba68323841dcdf0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Add a new group to the batch to run POA algorithm on. Based on the constraints of the batch, now all entries in a group may be added. This will be reflected in the per_seq_status of the call. Those entries that were added will be shown with a success.  <a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a8f2f44e7b4d7f51d8ba68323841dcdf0">More...</a><br /></td></tr>
<tr class="separator:a8f2f44e7b4d7f51d8ba68323841dcdf0"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:af2b27869811283b869700c181a75cfdc"><td class="memItemLeft" align="right" valign="top">virtual int32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#af2b27869811283b869700c181a75cfdc">get_total_poas</a> () const =0</td></tr>
<tr class="memdesc:af2b27869811283b869700c181a75cfdc"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get total number of partial order alignments in batch.  <a href="classclaragenomics_1_1cudapoa_1_1Batch.html#af2b27869811283b869700c181a75cfdc">More...</a><br /></td></tr>
<tr class="separator:af2b27869811283b869700c181a75cfdc"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a7387b746531d4e8ac1e5806ac2824f09"><td class="memItemLeft" align="right" valign="top"><a id="a7387b746531d4e8ac1e5806ac2824f09"></a>
virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a7387b746531d4e8ac1e5806ac2824f09">generate_poa</a> ()=0</td></tr>
<tr class="memdesc:a7387b746531d4e8ac1e5806ac2824f09"><td class="mdescLeft">&#160;</td><td class="mdescRight">Run partial order alignment algorithm over all POAs. <br /></td></tr>
<tr class="separator:a7387b746531d4e8ac1e5806ac2824f09"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a3224d1595caa5950c34708f4b7d64fe0"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">get_consensus</a> (std::vector&lt; std::string &gt; &amp;consensus, std::vector&lt; std::vector&lt; uint16_t &gt;&gt; &amp;coverage, std::vector&lt; <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">claragenomics::cudapoa::StatusType</a> &gt; &amp;output_status)=0</td></tr>
<tr class="memdesc:a3224d1595caa5950c34708f4b7d64fe0"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the consensus for each POA.  <a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">More...</a><br /></td></tr>
<tr class="separator:a3224d1595caa5950c34708f4b7d64fe0"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab39956c82d5d5a2d8df1b1695e15d9d2"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">get_msa</a> (std::vector&lt; std::vector&lt; std::string &gt;&gt; &amp;msa, std::vector&lt; <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> &gt; &amp;output_status)=0</td></tr>
<tr class="memdesc:ab39956c82d5d5a2d8df1b1695e15d9d2"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the multiple sequence alignments for each POA.  <a href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">More...</a><br /></td></tr>
<tr class="separator:ab39956c82d5d5a2d8df1b1695e15d9d2"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a0949cca1e89a40d759b0ca371512bb16"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">get_graphs</a> (std::vector&lt; <a class="el" href="classclaragenomics_1_1DirectedGraph.html">DirectedGraph</a> &gt; &amp;graphs, std::vector&lt; <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> &gt; &amp;output_status)=0</td></tr>
<tr class="memdesc:a0949cca1e89a40d759b0ca371512bb16"><td class="mdescLeft">&#160;</td><td class="mdescRight">Get the graph representation for each POA.  <a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">More...</a><br /></td></tr>
<tr class="separator:a0949cca1e89a40d759b0ca371512bb16"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ab807c4b01c2cddcdebb32952df13c0ec"><td class="memItemLeft" align="right" valign="top">virtual int32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">batch_id</a> () const =0</td></tr>
<tr class="memdesc:ab807c4b01c2cddcdebb32952df13c0ec"><td class="mdescLeft">&#160;</td><td class="mdescRight">Return batch ID.  <a href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">More...</a><br /></td></tr>
<tr class="separator:ab807c4b01c2cddcdebb32952df13c0ec"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aa8de262cb7c43d7219f7064bb700e7ae"><td class="memItemLeft" align="right" valign="top"><a id="aa8de262cb7c43d7219f7064bb700e7ae"></a>
virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html#aa8de262cb7c43d7219f7064bb700e7ae">reset</a> ()=0</td></tr>
<tr class="memdesc:aa8de262cb7c43d7219f7064bb700e7ae"><td class="mdescLeft">&#160;</td><td class="mdescRight">Reset batch. Must do before re-using batch. <br /></td></tr>
<tr class="separator:aa8de262cb7c43d7219f7064bb700e7ae"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Batched GPU CUDA POA object </p>
</div><h2 class="groupheader">Member Function Documentation</h2>
<a id="a8f2f44e7b4d7f51d8ba68323841dcdf0"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8f2f44e7b4d7f51d8ba68323841dcdf0">&#9670;&nbsp;</a></span>add_poa_group()</h2>

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          <td class="memname">virtual <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> claragenomics::cudapoa::Batch::add_poa_group </td>
          <td>(</td>
          <td class="paramtype">std::vector&lt; <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>per_seq_status</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">Group</a> &amp;&#160;</td>
          <td class="paramname"><em>poa_group</em>&#160;</td>
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          <td></td>
          <td>)</td>
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<p>Add a new group to the batch to run POA algorithm on. Based on the constraints of the batch, now all entries in a group may be added. This will be reflected in the per_seq_status of the call. Those entries that were added will be shown with a success. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">per_seq_status</td><td>Reference to an output vector of StatusType that holds the processing status of each entry in the group. NOTE: This API clears old entries in the vector. </td></tr>
    <tr><td class="paramname">poa_group</td><td>Vector of <a class="el" href="structclaragenomics_1_1cudapoa_1_1Entry.html" title="A structure to represent a sequence entry.">Entry</a>'s to process in POA. Based on the constraints of the batch, not all entries in a group may be added. This will be reflected in the per_seq_status of the call. Those entries that were added will show a success status. The POA algorithm will run with the sequences that were added.</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Status representing whether PoaGroup was successfully added to batch. </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#ab807c4b01c2cddcdebb32952df13c0ec">&#9670;&nbsp;</a></span>batch_id()</h2>

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          <td class="memname">virtual int32_t claragenomics::cudapoa::Batch::batch_id </td>
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          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<p>Return batch ID. </p>
<dl class="section return"><dt>Returns</dt><dd><a class="el" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a> ID </dd></dl>

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<a id="a3224d1595caa5950c34708f4b7d64fe0"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a3224d1595caa5950c34708f4b7d64fe0">&#9670;&nbsp;</a></span>get_consensus()</h2>

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          <td class="memname">virtual <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> claragenomics::cudapoa::Batch::get_consensus </td>
          <td>(</td>
          <td class="paramtype">std::vector&lt; std::string &gt; &amp;&#160;</td>
          <td class="paramname"><em>consensus</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">std::vector&lt; std::vector&lt; uint16_t &gt;&gt; &amp;&#160;</td>
          <td class="paramname"><em>coverage</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">std::vector&lt; <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">claragenomics::cudapoa::StatusType</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>output_status</em>&#160;</td>
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          <td>)</td>
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<p>Get the consensus for each POA. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">consensus</td><td>Reference to vector where consensus strings will be returned </td></tr>
    <tr><td class="paramname">coverage</td><td>Reference to vector where coverage of each base in each consensus string is returned </td></tr>
    <tr><td class="paramname">output_status</td><td>Reference to vector where the errors during kernel execution is captured</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Status indicating whether consensus generation is available for this batch. </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a0949cca1e89a40d759b0ca371512bb16">&#9670;&nbsp;</a></span>get_graphs()</h2>

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          <td class="memname">virtual void claragenomics::cudapoa::Batch::get_graphs </td>
          <td>(</td>
          <td class="paramtype">std::vector&lt; <a class="el" href="classclaragenomics_1_1DirectedGraph.html">DirectedGraph</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>graphs</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">std::vector&lt; <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>output_status</em>&#160;</td>
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          <td></td>
          <td>)</td>
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<p>Get the graph representation for each POA. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">graphs</td><td>Reference to a vector where directed graph of each poa is returned. </td></tr>
    <tr><td class="paramname">output_status</td><td>Reference to vector where the errors during kernel execution is captured </td></tr>
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  </dd>
</dl>

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<h2 class="memtitle"><span class="permalink"><a href="#ab39956c82d5d5a2d8df1b1695e15d9d2">&#9670;&nbsp;</a></span>get_msa()</h2>

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          <td class="memname">virtual <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> claragenomics::cudapoa::Batch::get_msa </td>
          <td>(</td>
          <td class="paramtype">std::vector&lt; std::vector&lt; std::string &gt;&gt; &amp;&#160;</td>
          <td class="paramname"><em>msa</em>, </td>
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          <td></td>
          <td class="paramtype">std::vector&lt; <a class="el" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>output_status</em>&#160;</td>
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<p>Get the multiple sequence alignments for each POA. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">msa</td><td>Reference to vector where msa strings of each poa is returned </td></tr>
    <tr><td class="paramname">output_status</td><td>Reference to vector where the errors during kernel execution is captured</td></tr>
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  </dd>
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<dl class="section return"><dt>Returns</dt><dd>Status indicating whether MSA generation is available for this batch. </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#af2b27869811283b869700c181a75cfdc">&#9670;&nbsp;</a></span>get_total_poas()</h2>

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          <td class="memname">virtual int32_t claragenomics::cudapoa::Batch::get_total_poas </td>
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          <td> const</td>
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<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
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<p>Get total number of partial order alignments in batch. </p>
<dl class="section return"><dt>Returns</dt><dd>Total POAs in batch. </dd></dl>

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<hr/>The documentation for this class was generated from the following file:<ul>
<li>cudapoa/include/claragenomics/cudapoa/<a class="el" href="batch_8hpp_source.html">batch.hpp</a></li>
</ul>
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